The complaint alleges that Cuomo appointed James Kiyonaga to the justice center’s No. 2 spot despite similar complaints at other state agencies. (Anthony DelMundo/New York Daily News)

A former special prosecutor under Gov. Cuomo filed a federal complaint Tuesday accusing a former state agency boss of sexual discrimination and retaliation.

Patricia Gunning, who had already complained internally about office misconduct at the state's Justice Center for the Protection of People with Special Needs, filed a claim with the U.S. Equal Employment Opportunity Commission.

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Gunning's complaint alleges that James Kiyonaga, the center's former acting executive director and executive deputy, engaged in a pattern of sexual discrimination, and that she was fired when she complained about the alleged abuse.

Gunning said Kiyonaga "fostered a sexualized frat boy culture," and that she was repeatedly subjected to her boss' "sexualized discussions of Justice Center employees."

She said Kiyonaga played favorites with women he was attracted to and romantically involved with, and that when she complained he screamed and cursed at her, changed her job duties and responsibilities and lied about her to the center's new executive director.

Patricia Gunning, a former special prosecutor at the Justice Center for the Protection of People with Special Needs, filed a federal complaint accusing Jay Kiyonaga of sexual descrimination and retaliation on May 29, 2018. (LinkedIn)

Gunning, in the complaint, says she was forced to resign in Aug. 2017 under duress.

The complaint alleges that Cuomo appointed Kiyonaga to the justice center's No. 2 spot despite similar complaints at other state agencies.

Kiyonaga currently works with the state's Office for People with Developmental Disabilities.

Kiyonaga has denied the charges. A spokesman for Cuomo's office did not immediately respond to a request for comment.